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<a href="../articles/animal_mobility.html">Cheatsheet: Animal Mobility File Format</a>
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<div class="hidden name"><code>mapMCDA.Rmd</code></div>
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<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">sp</span>)</pre></body></html></div>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">raster</span>)</pre></body></html></div>
<pre><code>## Loading required package: raster</code></pre>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rasterVis</span>)</pre></body></html></div>
<pre><code>## Loading required package: rasterVis</code></pre>
<pre><code>## Loading required package: lattice</code></pre>
<pre><code>## Loading required package: latticeExtra</code></pre>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">mapMCDA</span>)</pre></body></html></div>
<pre><code>## Loading required package: mapMCDA</code></pre>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
<p>Le package <code>mapMCDA</code> facilite la ponderation de plusieurs facteurs de risque pour produîre une carte de risque épidémiologique.</p>
<p>Néanmoins, l’expertise de l’utilisateur est cruciale. Elle s’exprime à trois niveaux :</p>
<ol style="list-style-type: decimal">
<li><p>Choix des facteurs de risque rélevants</p></li>
<li><p>Pour chaque facteur, mise en échelle commune de risque (e.g. entre 0 et 100)</p></li>
<li><p>Évaluation deux-à-deux de l’importance rélative des facteurs de risque</p></li>
</ol>
<p>À continuation, on utilise des cartes fournis par le package pour produîre une carte de risque d’exemple. <strong>Cette carte n’a aucun valeur épidémiologique.</strong></p>
</div>
<div id="facteurs-de-risque" class="section level1">
<h1 class="hasAnchor">
<a href="#facteurs-de-risque" class="anchor"></a>1. Facteurs de risque</h1>
<p>La fonction <code><a href="../reference/mapMCDA_datasets.html">mapMCDA_datasets()</a></code> permet de charger en mémoire toutes les cartes disponibles dans le package.</p>
<p>L’objet <code>cmr</code> est une simple liste de cartes : objets de type <code>Spatial*</code> pour les cartes vectoriels et de type <code>RasterLayer</code> pour les cartes raster.</p>
<p>Pour utiliser d’autre cartographie, utiliser les fonctions <code><a href="https://rdrr.io/pkg/rgdal/man/readOGR.html">rgdal::readOGR()</a></code> et <code><a href="https://rdrr.io/pkg/raster/man/raster.html">raster::raster()</a></code> respectivement pour des cartes vectoriels ou raster.</p>
<p>On peut aussi bénéficier de la fonction <code><a href="../reference/layer_type.html">layer_type()</a></code> pour charger tout type des cartes automatiquement, comme démontré dans le code commenté.</p>
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="no">cmr</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/mapMCDA_datasets.html">mapMCDA_datasets</a></span>()
<span class="co"># layers <- list.files(</span>
<span class="co"># system.file("cartography/CMR", package = "mapMCDA"),</span>
<span class="co"># full.names = TRUE</span>
<span class="co"># )</span>
<span class="co"># cmr <- lapply(layers, load_layer)</span>
<span class="co"># names(cmr) <- rmext(basename(layers)))</span></pre></body></html></div>
<p>L’une de ces cartes est celle des unités épidémiologiques, utilisée pour établir le cadre de travail.</p>
<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="no">unites_epi</span> <span class="kw"><-</span> <span class="no">cmr</span>$<span class="no">cmr_admin3</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/par.html">par</a></span>(<span class="kw">mar</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0</span>))
<span class="fu"><a href="https://rdrr.io/pkg/raster/man/plot.html">plot</a></span>(<span class="no">unites_epi</span>)</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/unite-epidemiologique-1.png" alt="Unités épidémiologiques d'exemple pour le Cameroun." width="700"><p class="caption">
Unités épidémiologiques d’exemple pour le Cameroun.
</p>
</div>
</div>
<a href="#mise-en-%C3%A9chelle" class="anchor"></a>2. Mise en échelle</h1>
<p>Chaque facteur de risque varie dans une échelle qui lui est propre. La densité animale, par exemple, varie entre 0 et presque 5500 têtes par <span class="math inline">\(km^2\)</span>.</p>
<p>Pour les cartes <em>vectorielles</em>, qui representent la localisation des entités spatiales telles que lacs ou forêts, on considère la <strong>distance</strong> à dites entités.</p>
<p>Ce package utilise pour l’instant une fonction linèaire pour la mise en échelle. Cependant, la rélation peut être directe ou inverse.</p>
<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/pkg/raster/man/plot.html">plot</a></span>(
<span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="kw">x</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">100</span>), <span class="kw">y</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0</span>, <span class="fl">100</span>)),
<span class="kw">type</span> <span class="kw">=</span> <span class="st">'l'</span>,
<span class="kw">xaxs</span> <span class="kw">=</span> <span class="st">"i"</span>,
<span class="kw">yaxs</span> <span class="kw">=</span> <span class="st">"i"</span>,
<span class="kw">xaxt</span> <span class="kw">=</span> <span class="st">"n"</span>,
<span class="kw">lab</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">7</span>),
<span class="kw">xlab</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Échelle originale"</span>),
<span class="kw">ylab</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Échelle de risque"</span>)
<span class="fu"><a href="https://rdrr.io/r/graphics/abline.html">abline</a></span>(<span class="fl">100</span>, -<span class="fl">1</span>)</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/mise-echelle-1.png" alt="Mis en échelle directe ou inverse." width="384"><p class="caption">
Mis en échelle directe ou inverse.
</p>
</div>
<p>La fonction <code><a href="../reference/risk_layer.html">risk_layer()</a></code> calcule la carte de risque associé à un facteur concret dans une échelle donnée. Par défault c’est entre 0 et 100. Pour inverser la rélation il suffit de passer les limits dans l’ordre inverse, e.g. <code><a href="https://rdrr.io/r/base/c.html">c(100, 0)</a></code>.</p>
<p>D’ailleurs, elle utilise la carte d’unités épidémiologiques pour établir les limits de calcul de risque.</p>
<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="no">risques</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(
<span class="kw">dens_animale</span> <span class="kw">=</span> <span class="fu"><a href="../reference/risk_layer.html">risk_layer</a></span>(
<span class="no">cmr</span>$<span class="no">animal.density</span>,
<span class="kw">boundaries</span> <span class="kw">=</span> <span class="no">unites_epi</span>
<span class="co"># , scale_target = c(0, 100) # échelle directe par défault</span>
),
<span class="kw">points_eau</span> <span class="kw">=</span> <span class="fu"><a href="../reference/risk_layer.html">risk_layer</a></span>(
<span class="no">cmr</span>$<span class="no">water_bodies</span>,
<span class="kw">boundaries</span> <span class="kw">=</span> <span class="no">unites_epi</span>,
<span class="kw">scale_target</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">100</span>, <span class="fl">0</span>) <span class="co"># échelle renversée</span>
<span class="kw">parcs</span> <span class="kw">=</span> <span class="fu"><a href="../reference/risk_layer.html">risk_layer</a></span>(
<span class="no">cmr</span>$<span class="no">national_parks</span>,
<span class="kw">boundaries</span> <span class="kw">=</span> <span class="no">unites_epi</span>,
<span class="kw">scale_target</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">100</span>, <span class="fl">0</span>) <span class="co"># échelle renversée</span>
<p>On voudrait examiner les cartes de risque ainsi calculées. Mais pour cela, il faut qu’elles soient <em>alignées</em>. C’est à dire, qu’elles aient les mêmes <em>extents</em>, <em>résolutions</em> et <em>projections</em>.</p>
<p>On peut se servir de la fonction <code><a href="../reference/align_layers.html">align_layers()</a></code> qui arrange tout ça pour nous. Noter que ce pas n’est pas nécessaire pour continuer, car cette fonction est automatiquement executée si besoin.</p>
<div class="sourceCode" id="cb15"><html><body><pre class="r"><span class="no">risques_alignes</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/align_layers.html">align_layers</a></span>(<span class="no">risques</span>)
<span class="fu"><a href="https://rdrr.io/pkg/rasterVis/man/levelplot-methods.html">levelplot</a></span>(<span class="fu"><a href="https://rdrr.io/pkg/raster/man/stack.html">stack</a></span>(<span class="no">risques_alignes</span>))</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/align-layers-1.png" alt="Niveaux de risque associé à chaque facteur." width="576"><p class="caption">
Niveaux de risque associé à chaque facteur.
</p>
</div>
</div>
<div id="pondération-des-facteurs-de-risque" class="section level1">
<a href="#pond%C3%A9ration-des-facteurs-de-risque" class="anchor"></a>3. Pondération des facteurs de risque</h1>
<p>Il y a 3 facteurs à considérer. Il faut comparer 2-à-2 leurs importances relatives en une échelle de 1 à 9 et representer ces rélations en une matrice qui doit avoir des 1 dans son diagonale.</p>
<p>Noter que les élements symmetriques doivent être réciproques.</p>
<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="no">M</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(
<span class="fl">1</span>, <span class="fl">6</span>, <span class="fl">4</span>,
<span class="fl">1</span>/<span class="fl">6</span>, <span class="fl">1</span>, <span class="fl">3</span>,
<span class="fl">1</span>/<span class="fl">4</span>, <span class="fl">1</span>/<span class="fl">3</span>, <span class="fl">1</span>
), <span class="kw">byrow</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="fl">3</span>, <span class="fl">3</span>)
<span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span>(<span class="no">M</span>) <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span>(<span class="no">M</span>) <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/raster/man/names.html">names</a></span>(<span class="no">risques</span>)
<span class="kw pkg">knitr</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html">kable</a></span>(<span class="no">M</span>, <span class="kw">digits</span> <span class="kw">=</span> <span class="fl">2</span>)</pre></body></html></div>
<th align="right">dens_animale</th>
<th align="right">points_eau</th>
<th align="right">parcs</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="right">1.00</td>
<td align="right">6.00</td>
<td align="right">4</td>
</tr>
<tr class="even">
<td align="right">0.17</td>
<td align="right">1.00</td>
<td align="right">3</td>
</tr>
<tr class="odd">
<td align="right">0.25</td>
<td align="right">0.33</td>
<td align="right">1</td>
</tr>
</tbody>
</table>
<p>Dans cette exemple, on considère que la densité animale est 6 fois plus importante que la distance aux points d’eau, et 4 fois plus importante que la distance aux parcs. Au même temps, que la distance aux points d’eau est 3 fois plus importante que celle aux parcs.</p>
<p>Le système calcule les coefficients de pondération les plus consistents avec ces valorations par paires, avec la fonction <code><a href="../reference/compute_weights.html">compute_weights()</a></code>.</p>
<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="no">w</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/compute_weights.html">compute_weights</a></span>(<span class="no">M</span>)</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/compute-weights-1.png" alt="Pondération des facteurs de risque." width="384"><p class="caption">
Pondération des facteurs de risque.
</p>
</div>
</div>
<div id="calcul-de-la-carte-de-risque" class="section level1">
<h1 class="hasAnchor">
<a href="#calcul-de-la-carte-de-risque" class="anchor"></a>4. Calcul de la carte de risque</h1>
<p>La fonction <code><a href="../reference/wlc.html">wlc()</a></code> (pour weighted linear combination) combine tous les facteurs de risque en utilisant les poids calculés précedament, et produise une carte de risque qui couvre toute la région.</p>
<div class="sourceCode" id="cb18"><html><body><pre class="r"><span class="no">risque_combine</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/wlc.html">wlc</a></span>(<span class="no">risques</span>, <span class="no">w</span>)
<span class="fu"><a href="https://rdrr.io/pkg/rasterVis/man/levelplot-methods.html">levelplot</a></span>(<span class="no">risque_combine</span>)</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/wlc-1.png" alt="Carte de risque combiné." width="576"><p class="caption">
Carte de risque combiné.
</p>
</div>
<p>Enfin, on peut produîre una carte par unité épidémiologique et dans une échelle de quelques niveaux de risque.</p>
<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="fu"><a href="../reference/risk_plot.html">risk_plot</a></span>(<span class="no">unites_epi</span>, <span class="fu"><a href="../reference/risk_unit.html">risk_unit</a></span>(<span class="no">risque_combine</span>, <span class="no">unites_epi</span>), <span class="kw">n</span> <span class="kw">=</span> <span class="fl">5</span>)</pre></body></html></div>
<div class="figure">
<img src="mapMCDA_files/figure-html/risk-plot-1.png" alt="Carte de niveaux de risque par unité épidémiologique." width="576"><p class="caption">
Carte de niveaux de risque par unité épidémiologique.
</p>
</div>
</div>
</div>
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